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Status
Public on May 27, 2003
Title
Kc167_Homotypic_R1_1
Sample type
RNA
Channel 1 Source name
Untreated Kc167 cells
Organism
Drosophila melanogaster Extracted molecule
total RNA
Channel 2 Source name
Untreated Kc167 cells
Organism
Drosophila melanogaster Extracted molecule
total RNA
Description
Total RNA was extracted from a dense culture of Kc167 cells which was maintained at 22C in Schneider's Complete Drosophila Medium (Invitrogen, Burlington, ON) supplemented with 5% Fetal Bovine Serum (Invitrogen) and 20ug/mL Gentamicin (Sigma, Oakville, ON) using Trizol Reagent (Invitrogen). 80ug of RNA, quantified by A260 in an Ultrmark plate reader (Biorad, Mississauga, ON), was used in each direct labeling reaction (see http://www.flyarrays.com ) to generate fluorescently labeled cDNA. The respective Cy3 and Cy5 targets were suspended in 75 uL DIG EasyHyb solution (Roche, Mississauga, ON)and were competitively hybridized to the array for 16 hours in a CMT-GAPS hybridization chamber (Corning, Acton, MA). Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings: 10uM scan: Cy3(543 nm) 100-72, Cy5(633 nm) 100-62 (laser power-PMT Gain). Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction. The data in the file is not normalized. The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Submission date
Apr 29, 2003
Last update date
Nov 21, 2005
Contact name
Zak Razak
E-mail(s)
z.razak@utoronto.ca Phone
905-569-4664
URL
http://www.flyarrays.com Organization name
University of Toronto
Department
Zoology Department
Lab
Canadian Drosophila Microarray Centre
Street address
3359 Mississauga Road
City
Mississauga
State/province
ON
ZIP/Postal code
L5L 1C6
Country
Canada
Platform ID
GPL311 Series (1)
GSE418 Kc167_Inter-slide_Variability_Test
Data table header descriptions ID_REF
CH1_RAW Raw fluorescence intensity - Cy3
CH1_BKD_RAW Raw background fluorescence intensity - Cy3
CH1_AREA Spot area - Cy3
Ch1_Signal_Noise_Ratio Signal to noise ratio - Cy3
CH2_RAW Raw fluorescence intensity - Cy5
CH2_BKD_RAW Raw background fluorescence intensity - Cy5
CH2_AREA Spot area - Cy5
Ch2_Signal_Noise_Ratio Signal to noise ratio - Cy5
Ignore Quality measure exported from GeneTraffic; flag=1, good=0
Ratio The ratio of CH2_Raw to CH1_Raw
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE The log2-transformed ratio of the Lowess-normalized fluorescence values (Ch2/Ch1) exported from GeneTraffic
Data table ID_REF CH1_RAW CH1_BKD_RAW CH1_AREA Ch1_Signal_Noise_Ratio CH2_RAW CH2_BKD_RAW CH2_AREA Ch2_Signal_Noise_Ratio Ignore Ratio VALUE UNF_VALUE 1
853.340454
53.05357
9400
7.08016
983.321411
25.464285
8400
14.487639
0
1.15232
-0.122120086
-0.122120086
2
926.079346
123.85714
12600
4.469087
1043.96875
16.214285
9600
22.367617
0
1.127299
-0.159857237
-0.159857237
3
1012.257446
498.892853
10100
0.476725
931.13916
20.107143
11500
20.046795
0
0.919864
-0.452675256
-0.452675256
4
959.217407
180.089279
13800
2.903023
1091.122192
26.857143
13100
12.559087
0
1.137513
-0.148437786
-0.148437786
5
2122.737061
94.625
15600
9.5942
2843
29.196428
13600
38.34522
0
1.339309
0.041003207
0.041003207
6
2388.991943
110.98214
12400
6.320875
3065.130859
21.714285
13000
48.801266
0
1.283023
-0.03026635
-0.03026635
7
881.033325
98.321426
12000
4.796552
1111.523804
15.732142
12600
21.44181
0
1.261614
0.00228164
0.00228164
8
875.231262
75.23214
14700
5.179993
1209.875
15.339286
12800
22.777644
0
1.382349
0.132846889
0.132846889
9
823.161072
137.660721
14900
3.063243
939.728943
6.732143
10700
45.564078
0
1.14161
-0.128555696
-0.128555696
10
813.700012
75.464287
9000
5.421719
977.813965
10.696428
8600
30.373913
0
1.201689
-0.057589037
-0.057589037
11
912.396851
73.785713
6300
6.35465
1360.282959
17.571428
5300
17.952347
0
1.49089
0.245369645
0.245369645
12
907.229736
75.339287
7400
5.301204
1692.808472
17.464285
4700
33.375395
0
1.865909
0.556060217
0.556060217
13
800.80188
69.76786
10600
4.627509
1063.848511
24.446428
9900
19.692438
0
1.328479
0.08197026
0.08197026
14
976.230774
42.05357
10400
9.863901
1357.43396
9.535714
10600
43.134191
0
1.390485
0.143627921
0.143627921
15
1249.115356
122.214287
13000
5.316883
1669.581421
6.357143
12900
57.295064
0
1.336611
0.055464843
0.055464843
16
1242.048584
167.75
14400
4.420171
1795.515137
17.732143
13200
29.212981
0
1.445608
0.167093634
0.167093634
17
3687.710449
134.875
14500
14.934157
5366.867676
28.25
15100
75.848166
0
1.455339
0.151684968
0.151684968
18
4028.159424
87.23214
13800
17.956314
6032.927246
27.964285
13700
79.581287
0
1.497688
0.194425862
0.194425862
19
1932.367798
229.803574
15500
4.940569
2583.701416
23.910715
13400
41.634166
0
1.337065
0.048404196
0.048404196
20
1690.720459
189.571426
16100
4.770006
2228.195557
38.589287
13800
29.033448
0
1.317897
0.04236706
0.04236706
16896 1845 Kbytes .Supplementary file Size Download File type/resource GSM6159_Cy3.Tif.gz
6.5 Mb
(ftp) (http) TIFF
GSM6159_Cy5.Tif.gz
5.6 Mb
(ftp) (http) TIFF
